CARMA statistics

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Protocols

CARMA specifications

Information


Unique identifier OMICS_01451
Name CARMA
Alternative name webCARMA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Lutz Krause

Information


Unique identifier OMICS_01451
Name CARMA
Alternative name webCARMA
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Lutz Krause

Publication for CARMA

CARMA citations

 (27)
call_split

Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates

2016
BMC Microbiol
PMCID: 4802719
PMID: 27001503
DOI: 10.1186/s12866-016-0669-8
call_split See protocol

[…] 1X10−1 and 80 % confidence level. The RDP classifier predicted the taxonomic origin of 16S rRNA up to the rank of genus. Moreover, in order to rectify diversity picture other reference databases such WebCARMA (based on Environmental gene tags i.e. EGTs) and non-redundant database M5NR were also used with standard parameters. […]

library_books

The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics

2015
Front Genet
PMCID: 4681832
PMID: 26734060
DOI: 10.3389/fgene.2015.00348

[…] f the earlier amplicon analysis programs were designed for Sanger or 454 ribosomal pyrotag sequences. For example, Mothur (Schloss et al., ), QIIME (Caporaso et al., ), MEGAN (Huson and Weber, ), and CARMA (Krause et al., ) are some of the legacy software still available. Nowadays, the software development for metagenomics considers short sequences like Illumina reads or very long sequences such a […]

library_books

Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities

2015
BMC Bioinformatics
PMCID: 4634789
PMID: 26537885
DOI: 10.1186/s12859-015-0788-5

[…] ays reads are classified by different methods. For example, MEGAN4 and MG-RAST make assignments based on bit-score as the sole parameter for judging significance. Other methods, such as DiScRIBinATE, CARMA3, and MetaPhyler, employ additional measures such as alignment parameter thresholds and/or a reciprocal BLAST search step, which have been shown to improve the accuracy of taxonomic assignments […]

call_split

Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India

2015
Front Microbiol
PMCID: 4620158
PMID: 26579081
DOI: 10.3389/fmicb.2015.01166
call_split See protocol

[…] and KEGG (Kanehisa and Goto, ) classification tree using SEED (May 17, 2010) and KEGG (Dec 1, 2010) identifiers, respectively. Additionally, taxonomic and functional annotation was carried out on the WebCARMA v1.0 online system (http://webcarma.cebitec.uni-bielefeld.de/cgi-bin/webcarma.cgi) (Gerlach et al., ). […]

library_books

Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes

2015
PMCID: 4571567
PMID: 26323759
DOI: 10.1098/rstb.2014.0328

[…] nal contigs with similar sequence patterns. For instance, MEGAN [] is based on homology searches, PhyloPythia/S/S+ [–] and ClaMS [] compare sequence compositions, such as oligonucleotide frequencies, CARMA [] performs phylogenetic reconstructions for sequence classification and PhymmBL [,] uses a combination of sequence composition and BLAST. Another hybrid approach, retrieving training sets from […]

library_books

One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes

2015
PMCID: 4713107
PMID: 26823635
DOI: 10.3767/003158515X689135

[…] rimers done at the CBS-KNAW Fungal Biodiversity Centre. The in silico pipeline for identifying suitable protein sequences for primer design is briefly described below.The approach was inspired by the CARMA algorithm for taxonomic identification of metagenomic sequences (). CARMA matches short environmental gene fragments to Pfam protein families and constructs a taxonomic profile for the sample. T […]

Citations

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CARMA institution(s)
Center for Biotechnology (CeBiTec), Bioinformatics Resource Facility (BRF), Bielefeld University, Bielefeld, Germany

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